% Stitch physical section 2, optical plane 1, channel 1:
>> IM=chessboardStitch([3,1],1); % IM is a structure
>> exploreChessBoard(IM) % (mouse wheel zooms, right-drag to pan )
>> exploreChessBoard(IM,2000) %Again but with a new threshold
% Say we want to rotate the tiles by -0.4 degrees and compare
% that with the original stitching:
% affineMatGen is in BakingTray
>> IM(2).params.affineMat = affineMatGen('rot', -0.4);
>> IM(2) = chessboardStitch([3,1],1,IM(2)); %To use new parameters
% Compare the two stitching results side by
>> exploreChessBoard(IM,2000)